On Thursday 31 August 2006 06:28, Takayuki KOTANI wrote: > addExplicitHydrogensToSatisfyValency does not work well using imidazole and > pyrrole.
Yes, that's a known problem. Resolving bond-orders from hybridization states, and common valencies is not trivial. Work is ongoing to get this working. For know, please do not use SMILES with implicit bond orders. That is, try to use "C1=NC=CN1" instead of "c1nccn1". An alternative, equally good approach, is to use a tool (e.g. OpenBabel) to convert the SMILES to, for example, a CML file and read the latter into the CDK. Sorry for the inconvenience :( I really hope we can get this fixed soon, but manpower is a problem here. Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
